Brain3D: Brain Report Automation via Inflated Vision Transformers in 3D

Radiology report generation has matured almost entirely on 2D chest radiographs, where the default route to better reports is a larger backbone or a pre-training one on medical data. We revisit that assumption on 3D multi-sequence brain MRI, a volumetric multi-disease regime, and find that the model is not the lever. Zero-shot medical and radiology vision-language models transfer poorly to brain MRI, with chest radiograph specialists failing most conspicuously, and five backbones fine-tuned identically across three model families and an order of magnitude in scale differ only marginally. What determines the quality of the report is the information injected into the prompt. We delegate perception to upstream 3D segmentation and classification, serialize their outputs into a structured fact sentence, and prompt a LoRA-adapted vision-language model with it; we call this PerFact. In a controlled study that fixes the backbone, data split, target reports, and adaptation while varying only the injected grounding, perception-derived facts outperform retrieved prior reports, retrieval becomes redundant once facts are present, and end-to-end predicted facts remain effective without any ground-truth annotation at inference. The residual gap between predicted and oracle facts is explained by the granularity of the facts rather than by the generator. Closed-ended visual question answering comes at no measurable cost to report quality, though the grounding source has little effect on it. On 3D brain MRI, grounding information, not model choice, is the dominant controllable factor in report quality.

Recent advances in radiology report generation (RRG) have been driven by large paired image-text datasets; however, progress in neuro-oncology has been limited due to a lack of open paired image-report datasets. Here, we introduce BTReport, an open-source framework for brain tumor RRG that constructs natural language radiology reports using deterministically extracted imaging features. Unlike existing approaches that rely on large general-purpose or fine-tuned vision-language models for both image interpretation and report composition, BTReport performs deterministic feature extraction for image analysis and uses large language models only for syntactic structuring and narrative formatting. By separating RRG into a deterministic feature extraction step and a report generation step, the generated reports are completely interpretable and less prone to hallucinations. We show that the features used for report generation are predictive of key clinical outcomes, including survival and IDH mutation status, and reports generated by BTReport are more closely aligned with reference clinical reports than existing baselines for RRG. Finally, we introduce BTReport-BraTS, a companion dataset that augments BraTS imaging with synthetically generated radiology reports produced with BTReport. Code for this project can be found at https://github.com/KurtLabUW/BTReport.

Recent advances in large language models (LLMs) and their extension to vision-language models (VLMs) have made it easier to combine text and images for tasks such as report generation. Existing VLMs in medicine typically focus on 2D images (chest X-rays), and their extension to 3D imaging has been difficult because of the lack of paired 3D imaging-text data. Thus, we introduce a new method for creating a 3D image-text dataset for brain oncology using 3D MRI scans of glioma and meningioma cases. We use a cooperative system in which several LLMs work together to generate and check reports, ensuring that they are accurate and clear. By leveraging the new 3D MRI-text dataset, we further build a VLM that converts MRI scans into tokens and aligns them with text instructions. Our VLM performed better in report generation and visual question answering tasks than other 2D and 3D methods. Our method not only improves the quality of reports but also helps with better diagnosis and treatment in brain oncology.